move and fix tests

lib/galaxy/dependencies/pinned-requirements.txt

@@ -49,7 +49,7 @@ cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
 cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12"
-conda_package_streaming==0.7.0 ; python_version >= "3.7" and python_version < "3.11"
+conda_package_streaming==0.7.0 ; python_version >= "3.7" and python_version < "3.12"
 cryptography==39.0.0 ; python_version >= "3.7" and python_version < "3.12"
 cwl-upgrader==1.2.4 ; python_version >= "3.7" and python_version < "3.12"
 cwl-utils==0.23 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/tool_util/deps/mulled/get_tests.py

@@ -9,6 +9,7 @@ import json
 import logging
 from glob import glob
 from typing import (
+    Any,
     Dict,
     Optional,
 )
@@ -38,7 +39,7 @@ INSTALL_JINJA_EXCEPTION = (
 )
 
 
-def get_commands_from_yaml(yaml_content):
+def get_commands_from_yaml(yaml_content: bytes) -> Optional[Dict[str, Any]]:
     """
     Parse tests from Conda's meta.yaml file contents
     """
@@ -83,7 +84,7 @@ def get_commands_from_yaml(yaml_content):
     return package_tests
 
 
-def get_run_test(file: str) -> Dict:
+def get_run_test(file: str) -> Dict[str, Any]:
     r"""
     Get tests from a run_test.sh file
     """
@@ -107,60 +108,20 @@ def prepend_anaconda_url(url):
     return f"https://anaconda.org{url}"
 
 
-def get_test_from_anaconda(url: str) -> Optional[Dict]:
+def get_test_from_anaconda(url: str) -> Optional[Dict[str, Any]]:
     """
     Given the URL of an anaconda tarball, return tests
-
-    >>> # test for info/recipe/meta.yaml
-    >>> tests = get_test_from_anaconda("https://anaconda.org/conda-forge/chopin2/1.0.6/download/noarch/chopin2-1.0.6-pyhd8ed1ab_0.tar.bz2")
-    >>> assert tests == {'commands': ['pip check', 'chopin2 --version'], 'imports': ['chopin2'], 'import_lang': 'python -c'}, tests
-    >>> tests = get_test_from_anaconda("https://anaconda.org/conda-forge/chopin2/1.0.7/download/noarch/chopin2-1.0.7-pyhd8ed1ab_1.conda")
-    >>> assert tests == {'commands': ['pip check', 'chopin2 --version'], 'imports': ['chopin2'], 'import_lang': 'python -c'}, tests
-    >>> # test for info/recipe/run_test.sh
-    >>> tests = get_test_from_anaconda("https://anaconda.org/bioconda/ucsc-pslmap/366/download/linux-64/ucsc-pslmap-366-hdd26221_0.tar.bz2")
-    >>> assert tests == {'commands': ['#!/bin/bash && pslMap 2> /dev/null || [[ "$?" == 255 ]] && ']}, tests
     """
     name, content = get_file_from_conda_package(
         url, ["info/recipe/meta.yaml", "info/recipe/meta.yaml.template", "info/recipe/run_test.sh"]
     )
-    if name.startswith("info/recipe/meta.yaml"):
+    if name and content and name.startswith("info/recipe/meta.yaml"):
         package_tests = get_commands_from_yaml(content)
         if package_tests:
             return package_tests
-    if name == "info/recipe/run_test.sh":
+    if name and content and name == "info/recipe/run_test.sh":
         return get_run_test(unicodify(content))
     return None
-    # try:
-    #     tarball = get_file_from_recipe_url(url)
-    # except tarfile.ReadError:
-    #     return None
-
-    # try:
-    #     metafile = tarball.extractfile("info/recipe/meta.yaml")
-    # except (tarfile.ReadError, KeyError, TypeError):
-    #     pass
-    # else:
-    #     package_tests = get_commands_from_yaml(metafile.read())
-    #     if package_tests:
-    #         return package_tests
-
-    # # this part is perhaps unnecessary, but some of the older tarballs have a testfile with .yaml.template ext
-    # try:
-    #     metafile = tarball.extractfile("info/recipe/meta.yaml.template")
-    # except (tarfile.ReadError, KeyError, TypeError):
-    #     pass
-    # else:
-    #     package_tests = get_commands_from_yaml(metafile)
-    #     if package_tests:
-    #         return package_tests
-
-    # # if meta.yaml was not present or there were no tests in it, try and get run_test.sh instead
-    # try:
-    #     run_test = tarball.extractfile("info/recipe/run_test.sh")
-    #     return get_run_test(run_test)
-    # except KeyError:
-    #     logging.info("run_test.sh file not present.")
-    #     return None
 
 
 def find_anaconda_versions(name, anaconda_channel="bioconda"):

lib/galaxy/tool_util/deps/mulled/mulled_build.py

@@ -18,7 +18,10 @@ import string
 import subprocess
 import sys
 from sys import platform as _platform
-from typing import List, TYPE_CHECKING
+from typing import (
+    List,
+    TYPE_CHECKING,
+)
 
 import yaml
 

test/unit/tool_util/mulled/test_get_tests.py

@@ -34,9 +34,9 @@ test:
 
 def test_get_commands_from_yaml():
     commands = get_commands_from_yaml(smart_str(TEST_RECIPE))
-    assert commands["imports"] == ["eagle"]
-    assert commands["commands"] == ["eagle --help"]
-    assert commands["import_lang"] == "python -c"
+    assert commands and commands["imports"] == ["eagle"]
+    assert commands and commands["commands"] == ["eagle --help"]
+    assert commands and commands["import_lang"] == "python -c"
 
 
 def test_get_run_test():
@@ -57,11 +57,26 @@ def test_prepend_anaconda_url():
 
 @external_dependency_management
 def test_get_test_from_anaconda():
+    # test old fashion tar.bz2 package
     tests = get_test_from_anaconda(
         "https://anaconda.org/bioconda/samtools/1.3.1/download/linux-64/samtools-1.3.1-5.tar.bz2"
     )
-    assert tests["commands"] == ["samtools --help"]
-    assert tests["import_lang"] == "python -c"
+    assert tests and tests["commands"] == ["samtools --help"]
+    assert tests and tests["import_lang"] == "python -c"
+
+    # test new conda package
+    tests = get_test_from_anaconda(
+        "https://anaconda.org/conda-forge/chopin2/1.0.7/download/noarch/chopin2-1.0.7-pyhd8ed1ab_1.conda"
+    )
+    assert tests and tests["commands"] == ["pip check", "chopin2 --version"]
+    assert tests and tests["imports"] == ["chopin2"]
+    assert tests and tests["import_lang"] == "python -c"
+
+    # test for package defining tests in info/recipe/run_test.sh
+    tests = get_test_from_anaconda(
+        "https://anaconda.org/bioconda/ucsc-pslmap/366/download/linux-64/ucsc-pslmap-366-hdd26221_0.tar.bz2"
+    )
+    assert tests and tests["commands"] == ['#!/bin/bash && pslMap 2> /dev/null || [[ "$?" == 255 ]] && ']
 
 
 @external_dependency_management